From ebc749c53f83b596bddbe4fbbae5c6f3a02654a8 Mon Sep 17 00:00:00 2001 From: mjoosten1 Date: Thu, 7 Nov 2024 14:41:21 +0100 Subject: [PATCH] fixed the RelionMetadataExporter now requiring the image.h5 file --- src/roodmus/simulation/run_parakeet.py | 32 +++++++++++++------------- 1 file changed, 16 insertions(+), 16 deletions(-) diff --git a/src/roodmus/simulation/run_parakeet.py b/src/roodmus/simulation/run_parakeet.py index ea99c3f..f04f820 100644 --- a/src/roodmus/simulation/run_parakeet.py +++ b/src/roodmus/simulation/run_parakeet.py @@ -1116,6 +1116,22 @@ def simulate_image( config.config_filename, sample_file=config.sample_filename ) + parakeet.simulate.exit_wave( + config.config_filename, + config.sample_filename, + exit_wave_file=config.exit_wave_filename, + ) + parakeet.simulate.optics( + config.config_filename, + exit_wave_file=config.exit_wave_filename, + optics_file=config.optics_filename, + ) + parakeet.simulate.image( + config.config_filename, + optics_file=config.optics_filename, + image_file=config.image_filename, + ) + # Write out the metadata if this is the first image in this # run_parakeet session or if overwrite requested if write_mtf: @@ -1144,22 +1160,6 @@ def simulate_image( ) ) - parakeet.simulate.exit_wave( - config.config_filename, - config.sample_filename, - exit_wave_file=config.exit_wave_filename, - ) - parakeet.simulate.optics( - config.config_filename, - exit_wave_file=config.exit_wave_filename, - optics_file=config.optics_filename, - ) - parakeet.simulate.image( - config.config_filename, - optics_file=config.optics_filename, - image_file=config.image_filename, - ) - # save the image os.system( "parakeet.export {} -o {}".format(